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Euryarchaeota

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Euryarchaeota
Halobacterium sp. strain NRC-1, each cell about 5 µm in length.
Scientific classification Edit this classification
Domain: Archaea
Kingdom: Euryarchaeota
Woese, Kandler & Wheelis, 1990[1]
Phyla[2]
Synonyms
  • non Euryarchaeota s.s. Garrity and Holt 2002
  • Euryarchaeida Luketa 2012
  • Methaneocreatrices Margulis & Schwartz 1982

Euryarchaeota (from Ancient Greek εὐρύς eurús, "broad, wide") is a kingdom of archaea.[3] Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines; halobacteria, which survive extreme concentrations of salt; and some extremely thermophilic aerobes and anaerobes, which generally live at temperatures between 41 and 122 °C. They are separated from the other archaeans based mainly on rRNA sequences and their unique DNA polymerase.[4]

Description

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The Euryarchaeota are diverse in appearance and metabolic properties. The phylum contains organisms of a variety of shapes, including both rods and cocci. Euryarchaeota may appear either gram-positive or gram-negative depending on whether pseudomurein is present in the cell wall.[5] Euryarchaeota also demonstrate diverse lifestyles, including methanogens, halophiles, sulfate-reducers, and extreme thermophiles in each.[5] Others live in the ocean, suspended with plankton and bacteria. Although these marine euryarchaeota are difficult to culture and study in a lab, genomic sequencing suggests that they are motile heterotrophs.[6]

Though it was previously thought that euryarchaeota only lived in extreme environments (in terms of temperature, salt content and/or pH), a paper by Korzhenkov et al. published in January 2019 showed that euryarchaeota also live in moderate environments, such as low-temperature acidic environments. In some cases, euryarchaeota outnumbered the bacteria present.[7] Euryarchaeota have also been found in other moderate environments such as water springs, marshlands, soil and rhizospheres.[8] Some euryarchaeota are highly adaptable; an order called Halobacteriales are usually found in extremely salty and sulfur-rich environments but can also grow in salt concentrations as low as that of seawater 2.5%.[8] In rhizospheres, the presence of euryarchaeota seems to be dependent on that of mycorrhizal fungi; a higher fungal population was correlated with higher euryarchaeotal frequency and diversity, while absence of mycorrihizal fungi was correlated with absence of euryarchaeota.[8]

Nomenclatural controversy

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In 2022, the proposed kingdom Methanobacteriati was introduced as a valid name for Euryarchaeota, which was claimed to be taxonomically invalid according to International Code of Nomenclature of Prokaryotes,[9] which gives priority to the first description of euryarchaeal cultivated species/genus (using the systematic suffix -ati for kingdom). This proposal is preferred by LPSN,[10] listing the Euryarchaeota as a not validly published phylum.[11]

The name Euryarchaeota is also currently considered as having no standing or validity according to the competitive SeqCode, which accepts descriptions of not cultivated taxa identified from sequence data.[12]

Euryarchaeota was listed in National Center for Biotechnology Information (NCBI) taxonomy browser[13] as a current name for phylum (Euryarchaeota Garrity and Holt 2002) till September 2024, considering Methanobacteriota as heterotypic synonym.[14] From October 2024 the names Methanobacteriati for kingdom and Halobacteriota, Methanobacteriota and Thermoplasmatota for included phyla are listed.[15]

The taxon Euryarchaeota is also listed in the Bergey's Manual of Systematics of Archaea and Bacteria.[16]

Euryarchaeota/Methanobacteriati is not listed as a taxon in the Genome Taxonomy Database (GTDB) applying not the level kingdom, even if it could be identified as a clade (Euryarchaeota s.s.).

Phylogeny

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16S rRNA based LTP_12_2021.[17][18][19]
Archaea

Other phylogenetic analyzes have suggested that the archaea of the clade DPANN may also belong to Euryarchaeota and that they may even be a polyphyletic group occupying different phylogenetic positions within Euryarchaeota. It is also debated whether the phylum Altiarchaeota should be classified in DPANN or Euryarchaeota.[20] A cladogram summarizing this proposal is graphed below.[21][22] The groups marked in quotes are lineages assigned to DPANN, but phylogenetically separated from the rest.

Dombrowski et al. 2019,[20] Jordan et al. 2017[21] and Cavalier-Smith 2020.[22]
Archaea

A third phylogeny, 53 marker proteins based GTDB 08-RS214.[23][24][25]

Archaea
Euryarchaeota s.s.

See also

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References

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  1. ^ Woese CR, Kandler O, Wheelis ML (June 1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
  2. ^ Castelle CJ, Banfield JF (2018). "Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life". Cell. 172 (6): 1181–1197. doi:10.1016/j.cell.2018.02.016. PMID 29522741.
  3. ^ Hogan CM (2010). E. Monosson, C. Cleveland (eds.). "Archaea". Encyclopedia of Earth. National Council for Science and the Environment. Retrieved 18 August 2017.
  4. ^ Lincoln SA, Wai B, Eppley JM, Church MJ, Summons RE, DeLong EF (July 2014). "Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean". Proceedings of the National Academy of Sciences of the United States of America. 111 (27): 9858–63. Bibcode:2014PNAS..111.9858L. doi:10.1073/pnas.1409439111. PMC 4103328. PMID 24946804.
  5. ^ a b Garrity GM, Holt JG (2015). "Euryarchaeota phy. nov.". In Whitman WB (ed.). Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons. doi:10.1002/9781118960608. ISBN 9781118960608.
  6. ^ Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV (February 2012). "Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota". Science. 335 (6068): 587–90. Bibcode:2012Sci...335..587I. doi:10.1126/science.1212665. PMID 22301318. S2CID 31381073.
  7. ^ Korzhenkov AA, Toshchakov SV, Bargiela R, Gibbard H, Ferrer M, Teplyuk AV, Jones DL, Kublanov IV, Golyshin PN, Golyshina OV (January 2019). "Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity". Microbiome. 7 (1): 11. doi:10.1186/s40168-019-0623-8. PMC 6350386. PMID 30691532.
  8. ^ a b c Bomberg M, Timonen S (October 2007). "Distribution of cren- and euryarchaeota in scots pine mycorrhizospheres and boreal forest humus". Microbial Ecology. 54 (3): 406–16. Bibcode:2007MicEc..54..406B. doi:10.1007/s00248-007-9232-3. PMID 17334967. S2CID 19425171.
  9. ^ Göker, Markus; Oren, Aharon (2024-01-22). "Valid publication of names of two domains and seven kingdoms of prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 74 (1). doi:10.1099/ijsem.0.006242. ISSN 1466-5026.
  10. ^ LPSN: Kingdom Methanobacteriati. Retrieved 25 September 2024.
  11. ^ LPSN: Phylum "Euryarchaeota". Retrieved 25 September 2024.
  12. ^ SeqCode Registry: “Euryarchaeota”. Retrieved 25 September 2024.
  13. ^ Sayers; et al. "Euryarchaeota (tree)". Taxonomy Browser. National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2024-09-25. Archived 2024-09-25 at the Wayback Machine
  14. ^ Sayers; et al. "Euryarchaeota". Taxonomy Browser. National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2024-09-25. Archived 2024-09-25 at the Wayback Machine
  15. ^ Sayers; et al. "Methanobacteriati". Taxonomy Browser. National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2024-10-10.
  16. ^ Bergey's Manual of Systematics of Archaea and Bacteria: A-Z Listing. Last updated: 27 March 2017. Wiley Online Library, John Wiley & Sons, Inc. Retrieved 25 September 2024.
  17. ^ "The LTP". Retrieved 23 February 2021.
  18. ^ "LTP_all tree in newick format". Retrieved 23 February 2021.
  19. ^ "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
  20. ^ a b Nina Dombrowski, Jun-Hoe Lee, Tom A Williams, Pierre Offre, Anja Spang (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. Nature.
  21. ^ a b Jordan T. Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd (2017). Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales. Frontiers.
  22. ^ a b Cavalier-Smith, Thomas; Chao, Ema E-Yung (2020). "Multidomain ribosomal protein trees and the planctobacterial origin of neomura (Eukaryotes, archaebacteria)". Protoplasma. 257 (3): 621–753. doi:10.1007/s00709-019-01442-7. PMC 7203096. PMID 31900730.
  23. ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 6 December 2021.
  24. ^ "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  25. ^ "Taxon History". Genome Taxonomy Database. Retrieved 6 December 2021.
  26. ^ Anja Spang, Eva F. Caceres, Thijs J. G. Ettema: Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. In: Science Volume 357 Issue 6351, eaaf3883, 11 Aug 2017, doi:10.1126/science.aaf3883
  27. ^ Sometines misspelled as Theinoarchaea: Catherine Badel, Gaël Erauso, Annika L. Gomez, Ryan Catchpole, Mathieu Gonnet, Jacques Oberto, Patrick Forterre, Violette Da Cunha: The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family. In: environmental microbiology. sfam 10 Sep 2019. doi:10.1111/1462-2920.14800
  28. ^ NCBI: Candidatus Poseidoniia (class)

Further reading

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